version.xml

<package name='Babel' version='0.4.2'>
    <depends on='BEAST.base' atleast='2.7.0'/>
    <depends on='BEAST.app' atleast='2.7.0'/>
	<depends on='BEASTLabs' atleast='2.0.0'/>
	
    <service type="beast.base.core.BEASTInterface">
        <provider classname="babel.CognateStats"/>
        <provider classname="babel.evolution.datatype.MutationDeathType"/>
        <provider classname="babel.evolution.datatype.TwoStateCovarionPlus"/>
        <provider classname="babel.evolution.likelihood.AbstractObservationProcess"/>
        <provider classname="babel.evolution.likelihood.ALSTreeLikelihood"/>
        <provider classname="babel.evolution.likelihood.AncestralStateLogger2"/>
        <provider classname="babel.evolution.likelihood.AnyTipObservationProcess"/>
        <provider classname="babel.evolution.likelihood.CognateCountThroughTimeLogger"/>
        <provider classname="babel.evolution.likelihood.LastStateRootProb"/>
        <provider classname="babel.evolution.likelihood.MultiSiteTreeLikelihood"/>
        <provider classname="babel.evolution.likelihood.SingleTipObservationProcess"/>
        <provider classname="babel.evolution.likelihood.TreeMixtureModel"/>
        <provider classname="babel.evolution.substitutionmodel.BirthDeathCovarion2"/>
        <provider classname="babel.evolution.substitutionmodel.BirthDeathModel"/>
        <provider classname="babel.evolution.substitutionmodel.ComplexMutationDeathModel"/>
        <provider classname="babel.evolution.substitutionmodel.NestedOrdinal"/>
        <provider classname="babel.evolution.substitutionmodel.NStatesNoRatesSubstitutionModel"/>
        <provider classname="babel.evolution.substitutionmodel.Ordinal"/>
        <provider classname="babel.nshelpers.AnnotationTuple"/>
        <provider classname="babel.nshelpers.AuthorMaintainer"/>
        <provider classname="babel.nshelpers.GenomeAnnotation"/>
        <provider classname="babel.nshelpers.NodeLocation"/>
        <provider classname="babel.preprocess.NexusFilter"/>
        <provider classname="babel.spanningtrees.SpanningTree"/>
        <provider classname="babel.tools.AddAscertainmentColumn"/>
        <provider classname="babel.tools.AdjustTipHeight"/>
        <provider classname="babel.tools.BinaryToMultiState"/>
        <provider classname="babel.tools.BinaryToMultiState2"/>
        <provider classname="babel.tools.centriod.BinnedMeanTree"/>
        <provider classname="babel.tools.centriod.ClusterRankTree"/>
        <provider classname="babel.tools.centriod.FrechetMeanCentroid"/>
        <provider classname="babel.tools.centriod.FrechetMeanTree"/>
        <provider classname="babel.tools.centriod.HalfWayMeanTree"/>
        <provider classname="babel.tools.ChangesThroughTimeCounter"/>
        <provider classname="babel.tools.CharsetlabelsToCharsets"/>
        <provider classname="babel.tools.CladeHeights"/>
        <provider classname="babel.tools.CladeMarker"/>
        <provider classname="babel.tools.CladeSetComparator"/>
        <provider classname="babel.tools.CladeSetCounter"/>
        <provider classname="babel.tools.CladeSetOverStateComparator"/>
        <provider classname="babel.tools.CognateSetRandomizer"/>
        <provider classname="babel.tools.CreateClusterTree"/>
        <provider classname="babel.tools.DeleteLanuageFromNexus"/>
        <provider classname="babel.tools.DolloAnnotator"/>
        <provider classname="babel.tools.dplace.ISOTreeParser"/>
        <provider classname="babel.tools.dplace.TreeConstraintProvider"/>
        <provider classname="babel.tools.dplace.TreeGrafter"/>
        <provider classname="babel.tools.DTARatesVisualiser"/>
        <provider classname="babel.tools.FamilyFilter"/>
        <provider classname="babel.tools.FamilyPruner"/>
        <provider classname="babel.tools.Fasta2Nexus"/>
        <provider classname="babel.tools.GetCladeMetaData"/>
        <provider classname="babel.tools.GetDescription"/>
        <provider classname="babel.tools.IllegalTreeCleaner"/>
        <provider classname="babel.tools.Json2Newick"/>
        <provider classname="babel.tools.Json2Nexus"/>
        <provider classname="babel.tools.LeafSplitter"/>
        <provider classname="babel.tools.LineagesThroughTimeCounter"/>
        <provider classname="babel.tools.MakeUltraMetric"/>
        <provider classname="babel.tools.MatrixVisualiser"/>
        <provider classname="babel.tools.MatrixVisualiserBase"/>
        <provider classname="babel.tools.MetaDataMerger"/>
        <provider classname="babel.tools.MRCAFinder"/>
        <provider classname="babel.tools.Newick2Nexus"/>
        <provider classname="babel.tools.NextStream2Newick"/>
        <provider classname="babel.tools.Nexus2AlignmentInJson"/>
        <provider classname="babel.tools.Nexus2Fasta"/>
        <provider classname="babel.tools.Nexus2Json"/>
        <provider classname="babel.tools.Nexus2Newick"/>
        <provider classname="babel.tools.NexusToCharsets"/>
        <provider classname="babel.tools.NodeAnnotator"/>
        <provider classname="babel.tools.PhonemeSimulator"/>
        <provider classname="babel.tools.Phy2Nexus"/>
        <provider classname="babel.tools.SpeciesTreeDistanceLogger"/>
        <provider classname="babel.tools.StateTransitionCounter"/>
        <provider classname="babel.tools.TaxonFilter"/>
        <provider classname="babel.tools.TimeSeriesPlot"/>
        <provider classname="babel.tools.TreeBootstrapESS"/>
        <provider classname="babel.tools.TreeEpochScaler"/>
        <provider classname="babel.tools.TreeESS"/>
        <provider classname="babel.tools.TreeMerger"/>
        <provider classname="babel.tools.TreeRelabeller"/>
        <provider classname="babel.tools.Trees2HeightLog"/>
        <provider classname="babel.tools.TreeScalerApp"/>
        <provider classname="babel.tools.TreeTransitionMarker"/>
        <provider classname="babel.tools.XML2Fasta"/>
        <provider classname="babel.tools.XML2Nexus"/>
        <provider classname="babel.util.SiteLikelihoodLogger"/>
        <provider classname="babel.util.SiteRateLogger"/>
    </service>

    <service type="beast.base.evolution.datatype.DataType">
        <provider classname="babel.evolution.datatype.MutationDeathType"/>
        <provider classname="babel.evolution.datatype.TwoStateCovarionPlus"/>
    </service>
	
	<map from="beast.evolution.datatype.MutationDeathType" to="babel.evolution.datatype.MutationDeathType"/>
	<map from="beast.evolution.datatype.TwoStateCovarionPlus" to="babel.evolution.datatype.TwoStateCovarionPlus"/>

	<map from="beast.evolution.substitutionmodel.BirthDeathCovarion2" to="babel.evolution.substitutionmodel.BirthDeathCovarion2"/>
	<map from="beast.evolution.BirthDeathModel" to="babel.evolution.substitutionmodel.BirthDeathModel"/>
	<map from="beast.evolution.ComplexMutationDeathModel" to="babel.evolution.substitutionmodel.ComplexMutationDeathModel"/>
	<map from="beast.evolution.NStatesNoRatesSubstitutionModel" to="babel.evolution.substitutionmodel.NStatesNoRatesSubstitutionModel"/>
	<map from="beast.evolution.NestedOrdinal" to="babel.evolution.substitutionmodel.NestedOrdinal"/>
	<map from="beast.evolution.Ordinal" to="babel.evolution.substitutionmodel.Ordinal"/>
	
	<map from="beast.evolution.likelihood.ALSTreeLikelihood" to="babel.evolution.likelihood.ALSTreeLikelihood"/>
	<map from="beast.evolution.likelihood.AbstractObservationProcess" to="babel.evolution.likelihood.AbstractObservationProcess"/>
	<map from="beast.evolution.likelihood.AncestralStateLogger2" to="babel.evolution.likelihood.AncestralStateLogger2"/>
	<map from="beast.evolution.likelihood.AnyTipObservationProcess" to="babel.evolution.likelihood.AnyTipObservationProcess"/>
	<map from="beast.evolution.likelihood.CognateCountThroughTimeLogger" to="babel.evolution.likelihood.CognateCountThroughTimeLogger"/>
	<map from="beast.evolution.likelihood.LastStateRootProb" to="babel.evolution.likelihood.LastStateRootProb"/>
	<map from="beast.evolution.likelihood.MultiSiteTreeLikelihood" to="babel.evolution.likelihood.MultiSiteTreeLikelihood"/>
	<map from="beast.evolution.likelihood.PartialsProvider" to="babel.evolution.likelihood.PartialsProvider"/>
	<map from="beast.evolution.likelihood.SingleTipObservationProcess" to="babel.evolution.likelihood.SingleTipObservationProcess"/>
	<map from="beast.evolution.likelihood.TreeMixtureModel" to="babel.evolution.likelihood.TreeMixtureModel"/>
	
	<packageapp description="CognateStats"
              class="babel.CognateStats"
              args=""
              icon="babel/icons/CognateStats.png"
            />
    <packageapp description="SpanningTree"
              class="babel.spanningtrees.SpanningTree"
              args=""
              icon="babel/icons/SpanningTree.png"
            />
    <packageapp
    		  description="filters all leafs from specified taxon sets out of a tree file based on clade membership"
              class="babel.tools.FamilyFilter"
              args=""
            />
    <packageapp description="Match clades from two tree sets and print support for both sets"
              class="babel.tools.CladeSetComparator"
              args=""
            />
    <packageapp description="Counts number of distinct clades in a tree set"
              class="babel.tools.CladeSetCounter"
              args=""
            />
    <packageapp description="Estimate ESS for a tree posterior sample (as produced by BEAST)"
              class="babel.tools.TreeESS"
              args=""
            />
    <packageapp description="Convert NEXUS tree file"
              class="babel.tools.Nexus2Newick"
              args=""
            />
    <packageapp description="Convert NEXUS alignment file into json file with alignemnt that can be used in BEAST with the -DF option"
              class="babel.tools.Nexus2AlignmentInJson"
              args=""
            />
    <packageapp description="Convert newick tree file"
              class="babel.tools.Newick2Nexus"
              args=""
            />

  <packageapp description="Reports exception-throwing trees in a tree file"
              class="babel.tools.IllegalTreeCleaner"
              args=""
            />
    <packageapp description="Convert BEAST XML file into NEXUS alignemnt file"
              class="babel.tools.XML2Nexus"
              args=""
            />
    <packageapp description="Convert BEAST XML file into fasta alignemnt file"
              class="babel.tools.XML2Fasta"
              args=""
            />
    <packageapp description="Convert NEXUS alignment file into fasta alignemnt file"
              class="babel.tools.Nexus2Fasta"
              args=""
            />
    <packageapp description="Convert FASTA file into NEXUS alignemtn file"
              class="babel.tools.Fasta2Nexus"
              args=""
            />
    <packageapp description="Convert phyml phy format to nexus alignment file"
              class="babel.tools.Phy2Nexus"
              args=""
            />
    <packageapp description="Set tip heights of existing tree to match the heights from a list"
              class="babel.tools.AdjustTipHeight"
              args=""
            />
    <packageapp description="Relabels leafs of tree set, and splits leafs into random binary sub-tree with branch lengths exponentially distributed"
              class="babel.tools.LeafSplitter"
              args=""
            />
    <packageapp description="TreeGrafter"
              class="babel.tools.dplace.TreeGrafter"
              args=""
            />
    <packageapp description="TaxonReplacer"
              class="babel.tools.dplace.TaxonReplacer"
              args=""
            />
    <packageapp description="Relabels taxa in a tree file. Usfeful for instance when labels are iso codes and language names are required for visualisation"
              class="babel.tools.TreeRelabeller"
              args=""
            />
    <packageapp description="Annotates nodes in a tree."
              class="babel.tools.NodeAnnotator"
              args=""
            />
    <packageapp description="Mark specific transitions of a meta-data attribute on a tree to make it easy to visualise these transitions"
              class="babel.tools.TreeTransitionMarker"
              args=""
            />
    <packageapp description="Converts a rooted tree (set) to an ultrametric tree (set)"
              class="babel.tools.MakeUltraMetric"
              args=""
            />
    <packageapp description="Scales trees so epochs have the same length"
              class="babel.tools.TreeEpochScaler"
              args=""
            />
    <packageapp description="Produce table for lineages through time plot with 95%HPD bounds"
              class="babel.tools.LineagesThroughTimeCounter"
              args=""
            />
    <packageapp description="Prints description of a BEAST class"
              class="babel.tools.GetDescription"
              args=""
            />
    <packageapp description="Counts transitions of tags along branches of a tree"
              class="babel.tools.StateTransitionCounter"
              args=""
            />
    <packageapp description="Draw time series plot to png or pdf"
              class="babel.tools.TimeSeriesPlot"
              args=""
            />
    <packageapp
    		  description="Filters all leafs from specified taxon sets out of a tree file based on list of taxa to include"
              class="babel.tools.TaxonFilter"
              args=""
            />
    <packageapp
    		  description="Create SVG files to visualise rates for a discrete rate analysis"
              class="babel.tools.DTARatesVisualiser"
              args=""
            />
    <packageapp
    		  description="Annotate tree with k-Dollo information and calculate Dollo-k characters"
              class="babel.tools.DolloAnnotator"
              args=""
            />
    <packageapp
    		  description="Creates UPGMA, NJ or other cluster tree from an alignment and save to newick format"
              class="babel.tools.CreateClusterTree"
              args=""
            />
    <packageapp
    		  description="Scales trees with given scale factor or a desired height"
              class="babel.tools.TreeScalerApp"
              args=""
            />
    <packageapp
    		  description="Create trace log of tree distances between species tree and its gene trees"
              class="babel.tools.SpeciesTreeDistanceLogger"
              args=""
            />
    <packageapp
          description="MRCAFinder Finds MRCA of set of nodes in a tree log."
              class="babel.tools.MRCAFinder"
              args=""
            />
    <packageapp
          description="Add `cartoon` annotations to summary tree, so FigTree shows them as triangle"
              class="babel.tools.TreeCartooniser"
              args=""
            />
    <packageapp
          description="Produce statistics on taxa that form the sister clade of a given clade"
              class="babel.tools.SisterCladeCounter"
              args=""
            />
    <packageapp
          description="Estimate migration speed for a tree posterior sample of phylogeographic analysis (as produced by BEAST)"
              class="babel.tools.SpeedCalculator"
              args=""
            />
    <packageapp
          description="Extract clade heights from tree posterior sample (as produced by BEAST)"
              class="babel.tools.CladeHeights"
              args=""
            />
</package>